diff --git a/letta/llm_api/anthropic_client.py b/letta/llm_api/anthropic_client.py
index bab45f9c..c0f7a39b 100644
--- a/letta/llm_api/anthropic_client.py
+++ b/letta/llm_api/anthropic_client.py
@@ -110,7 +110,9 @@ class AnthropicClient(LLMClientBase):
         ]
 
         # Move 'system' to the top level
-        # assert data["messages"][0]["role"] == "system", f"Expected 'system' role in messages[0]:\n{data['messages'][0]}"
+        if data["messages"][0]["role"] != "system":
+            raise RuntimeError(f"First message is not a system message, instead has role {data["messages"][0]["role"]}")
+
         data["system"] = data["messages"][0]["content"]
         data["messages"] = data["messages"][1:]
 
diff --git a/letta/llm_api/llm_client_base.py b/letta/llm_api/llm_client_base.py
index cab01dce..66cbf244 100644
--- a/letta/llm_api/llm_client_base.py
+++ b/letta/llm_api/llm_client_base.py
@@ -42,7 +42,6 @@ class LLMClientBase:
         Otherwise returns a ChatCompletionResponse.
         """
         request_data = self.build_request_data(messages, tools, tool_call)
-        response_data = {}
 
         try:
             log_event(name="llm_request_sent", attributes=request_data)
diff --git a/letta/serialize_schemas/marshmallow_agent.py b/letta/serialize_schemas/marshmallow_agent.py
index f38f1921..a6fb330f 100644
--- a/letta/serialize_schemas/marshmallow_agent.py
+++ b/letta/serialize_schemas/marshmallow_agent.py
@@ -59,29 +59,26 @@ class MarshmallowAgentSchema(BaseSchema):
         """
         - Removes `message_ids`
         - Adds versioning
-        - Marks messages as in-context
+        - Marks messages as in-context, preserving the order of the original `message_ids`
         - Removes individual message `id` fields
         """
         data = super().sanitize_ids(data, **kwargs)
         data[self.FIELD_VERSION] = letta.__version__
 
-        message_ids = list(data.pop(self.FIELD_MESSAGE_IDS, []))
+        original_message_ids = data.pop(self.FIELD_MESSAGE_IDS, [])
+        messages = data.get(self.FIELD_MESSAGES, [])
 
-        # NOTE: currently we don't support out-of-context messages since it has a bunch of system message spams
-        # TODO: support out-of-context messages
-        messages = []
+        # Build a mapping from message id to its first occurrence index and remove the id in one pass
+        id_to_index = {}
+        for idx, message in enumerate(messages):
+            msg_id = message.pop(self.FIELD_ID, None)
+            if msg_id is not None and msg_id not in id_to_index:
+                id_to_index[msg_id] = idx
 
-        # loop through message in the *same* order is the in-context message IDs
-        data[self.FIELD_IN_CONTEXT_INDICES] = []
-        for i, message in enumerate(data.get(self.FIELD_MESSAGES, [])):
-            # if id matches in-context message ID, add to `messages`
-            if message[self.FIELD_ID] in message_ids:
-                data[self.FIELD_IN_CONTEXT_INDICES].append(i)
-            messages.append(message)
+        # Build in-context indices in the same order as the original message_ids
+        in_context_indices = [id_to_index[msg_id] for msg_id in original_message_ids if msg_id in id_to_index]
 
-        # remove ids
-        for message in messages:
-            message.pop(self.FIELD_ID, None)  # Remove the id field
+        data[self.FIELD_IN_CONTEXT_INDICES] = in_context_indices
         data[self.FIELD_MESSAGES] = messages
 
         return data
diff --git a/tests/integration_test_experimental.py b/tests/integration_test_experimental.py
index cbc5ab74..23489895 100644
--- a/tests/integration_test_experimental.py
+++ b/tests/integration_test_experimental.py
@@ -337,9 +337,7 @@ def test_multi_agent_broadcast_client(client: Letta, weather_tool):
             }
         ],
     )
-    import ipdb
 
-    ipdb.set_trace()
     for message in response.messages:
         print(message)
 
diff --git a/tests/test_agent_serialization.py b/tests/test_agent_serialization.py
index d73bffb1..ef455ee9 100644
--- a/tests/test_agent_serialization.py
+++ b/tests/test_agent_serialization.py
@@ -604,3 +604,41 @@ def test_agent_download_upload_flow(fastapi_client, server, serialize_test_agent
         agent_id=copied_agent_id,
         messages=[MessageCreate(role=MessageRole.user, content="Hello copied agent!")],
     )
+
+
+# TODO: Add this back
+# @pytest.mark.parametrize("test_af_filename", ["deep_research_agent.af"])
+# def test_agent_file_upload_flow(fastapi_client, server, default_user, other_user, test_af_filename):
+#     """
+#     Test the full E2E serialization and deserialization flow using FastAPI endpoints.
+#     """
+#     file_path = Path(__file__).parent / "test_agent_files" / test_af_filename
+#     with open(file_path, "r") as f:
+#         data = json.load(f)
+#
+#     # Ensure response matches expected schema
+#     agent_schema = AgentSchema.model_validate(data)  # Validate as Pydantic model
+#     agent_json = agent_schema.model_dump(mode="json")  # Convert back to serializable JSON
+#
+#     import ipdb;ipdb.set_trace()
+#
+#     # Step 2: Upload the serialized agent as a copy
+#     agent_bytes = BytesIO(json.dumps(agent_json).encode("utf-8"))
+#     files = {"file": ("agent.json", agent_bytes, "application/json")}
+#     upload_response = fastapi_client.post(
+#         "/v1/agents/import",
+#         headers={"user_id": other_user.id},
+#         params={"append_copy_suffix": True, "override_existing_tools": False, "project_id": None},
+#         files=files,
+#     )
+#     assert upload_response.status_code == 200, f"Upload failed: {upload_response.text}"
+#
+#     copied_agent = upload_response.json()
+#     copied_agent_id = copied_agent["id"]
+#
+#     # Step 3: Ensure copied agent receives messages correctly
+#     server.send_messages(
+#         actor=other_user,
+#         agent_id=copied_agent_id,
+#         messages=[MessageCreate(role=MessageRole.user, content="Hello copied agent!")],
+#     )